CN113025745B - 一种用于检测小麦成株期抗白粉病基因PmBMYD的KASP引物及其应用 - Google Patents
一种用于检测小麦成株期抗白粉病基因PmBMYD的KASP引物及其应用 Download PDFInfo
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- CN113025745B CN113025745B CN202110448818.XA CN202110448818A CN113025745B CN 113025745 B CN113025745 B CN 113025745B CN 202110448818 A CN202110448818 A CN 202110448818A CN 113025745 B CN113025745 B CN 113025745B
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Abstract
本发明涉及一种用于检测小麦成株期抗白粉病基因PmBMYD的KASP引物及其应用。抗白粉病基因PmBMYD的核苷酸序列如SEQ.ID.NO:1所示KASP引物组成：F1 如SEQ.ID.NO:3所示；F2如SEQ.ID.NO:4所示；R如SEQ.ID.NO:5所示；特异荧光序列FAM如SEQ.ID.NO:6所示；特异荧光序列HEX如SEQ.ID.NO:7所示。上述KASP引物使用方法如下：以待测小麦的基因组DNA为模板，用所述的KASP引物进行PCR扩增，然后根据检测到的荧光颜色判断样品基因型类型，红色表示基因型为CC，蓝色表示基因型为TT。携有基因型TT的材料抗性显著优于携带基因型CC的材料。上述的KASP引物可在小麦抗白粉病分子辅助育种中进行应用，以缩短抗白粉病材料的育种周期。
Description
技术领域
本发明属于生物技术领域，具体涉及一种用于检测小麦成株期抗白粉病基因PmBMYD的KASP引物及其应用。
背景技术
小麦白粉病是由禾谷类白粉菌Blumeria graminis f.sp.tritici(Bgt)引起的一种世界性叶部病害，主要发生在气候湿润和凉爽的地区，比如中国、欧洲和南美洲的南锥地区。受到白粉病侵害的麦田可减产5％～62％，此外还严重影响了面粉质量。
第一次绿色革命后，随着小麦植株高度矮化，种植密度加大及水肥条件的改善，为小麦白粉病的发生和传播创造了更为有利的条件，使得发病面积逐步扩大。我国小麦白粉病主要发生地由云南、贵州、四川等湿润的西南地区及山东沿海地区向北方日趋蔓延。1991年小麦白粉病在全国25个省、市和自治区大范围流行，感病面积达1227万公顷，直接造成小麦减产7.7亿公斤。2009至2018近十年小麦白粉病发病面积平均每年约10000万亩。喷洒农药虽是目前防御病害的主要方法，但同时也加速了病原菌生理小种的变异，使问题变的更加复杂。抗病品种的培育和利用一直被认为是最经济、绿色有效的防治方式。
小麦白粉病抗性基因可以分为质量抗病基因(也称苗期抗病基因)和数量抗病基因(也称成株期抗病基因)，质量抗性是针对一个或几个生理小种表现出较高水平且全生育期的抗性，对其他的白粉菌生理小种没有抗性，符合Flor提出的“基因对基因”假说；数量抗性则是对所有白粉菌生理小种表现一定的抗性，抗性水平较低，且只在小麦成株期表现。研究表明培育携有成株期抗病基因或QTL的品种具有更好的抗病性，聚合三个部分抗性基因的小麦品系能达到对白粉病免疫的水平，在实际育种中具有更大的价值。但成株期小麦抗白粉病基因报道很少，目前发表被正式命名的68个小麦抗白粉病(Pm1～Pm68)中只有Pm38、Pm39和Pm46属于成株期抗病基因。因此进一步挖掘成株期白粉病抗性位点及开发其连锁分子标记对于小麦抗白粉病育种实践具有重大意义。
发明内容
本发明提出了一种用于检测小麦成株期抗白粉病基因PmBMYD的KASP引物，所述的KASP引物在小麦抗白粉病分子辅助育种中是可用的。
本发明的技术方案为：
本发明提供的一种用于检测小麦成株期抗白粉病基因PmBMYD的KASP引物，所述抗白粉病基因PmBMYD为核苷酸序列SEQ.ID.NO:1所示的DNA序列，该基因位于小麦染色体小麦3BL上；
所述KASP引物由以下序列组成：F1如SEQ.ID.NO:3所示，F2如SEQ.ID.NO:4所示，R如SEQ.ID.NO:5所示。具体的：
F1：5’-GAAGGTGACCAAGTTCATGCTTTGGAGGGGCTCCGACAAT-3’；
F2：5’-GAAGGTCGGAGTCAACGGATTTTGGAGGGGCTCCGACAAC-3’；
R：5’-TCCACCACCAGTAGCTCCACACCACTCCAG-3’；
特异荧光序列FAM如SEQ.ID.NO:6所示，特异荧光序列HEX如SEQ.ID.NO:7所示，具体的：
特异荧光序列FAM：5’-GAAGGTGACCAAGTTCATGCT-3’；
特异荧光序列HEX：5’-GAAGGTCGGAGTCAACGGATT-3’。
进一步的，所述抗白粉病基因PmBMYD表达的蛋白为氨基酸序列SEQ.ID.NO:2所示的蛋白。
本发明还提供了上述的KASP引物对检测小麦成株期抗白粉病基因型的方法，包括如下步骤：
以待测小麦的基因组DNA为模板，用所述的KASP引物进行PCR扩增，然后根据检测到的荧光颜色判断样品基因型类型，红色表示基因型为CC，蓝色表示基因型为TT。携有基因型TT的材料抗性显著优于携带基因型CC的材料。
本发明还提供了鉴定上述小麦成株期抗白粉病基因型的试剂盒，所述试剂盒含有所述KASP引物。
上述的KASP引物可在小麦抗白粉病分子辅助育种中进行应用，以缩短抗白粉病材料的育种周期。
本发明的有益效果为：
本发明实施例在以携有优异抗病等位位点T的抗病材料白蚂蚁蛋和含有感病等位位点C感病材料濮麦9号的两个亲本构建的155株F2群体中进行基因分型。分型结果分布为含基因型TT的有40个株系，携有TC的69个，CC的46个(见表3)，分离比符合1:2:1(χ2＝2.329，P-value＝0.3121)，说明设计的KASP引物是有效的。通过进一步统计各基因型中平均白粉病抗性情况，携有基因型TT，TC和CC的材料平均得分为1.53±1.05、1.59±1.05和2.06±1.31(P-value<0.05)，说明KASP引物在小麦抗白粉病分子辅助育种中是可用的。
附图说明
图1为(a)2017，(b)2018,(c)2019,(d)2020和(e)BLUP值环境中河南省小麦核心种质资源白粉病抗性全基因关联分析的曼哈顿图。横坐标1～7代表1A～7A，8～14代表1B～7B，15～21代表1D～7D。水平虚线表示关联分析结果中显著阈值LOD＝3。PmBMYD(Qpm-3B)是在本申请中发现的新基因。
图2为TraesCS3B01G483700.1和RGA S-L8两基因蛋白序列比对图。
图3为携有优异抗病等位位点T的抗病材料白蚂蚁蛋和含有感病等位位点C感病材料濮麦9号的两个亲本构建的155株F2群体基因分型图。图中红色表示基因型为CC的F2单株，蓝色表示基因型为TT的F2单株。
具体实施方式
下面通过具体实施方式对本发明进行更加详细的说明，以便于对本发明技术方案的理解，但并不用于对本发明保护范围的限制。
术语解释：Kasp标记是根据基因序列中单个碱基的不同来设计的特异性引物，通常是将具有多态性的核苷酸位点设计在引物的3’端、将与通用荧光引物结合后能发出不同颜色的FAM序列标签和HEX序列标签设计在引物5’端，基于ARMPCR原理，用通用的荧光引物进行扩增，根据检测到信号的颜色来判断单个核苷酸的多态性。
一、成株期抗白粉病基因PmBMYD的鉴定
为了快速鉴定一批新的小麦成株期白粉病抗性基因和种质资源，用小麦660K芯片对由371份小麦农家种和266份释放品种组成的637份河南省小麦核心种质(所述637份河南省小麦核心种质均由河南省农业科学院分子育种室提供，公众可从河南省农业科学院分子育种室获得)，进行了基因分型并结合2017至2020四年田间小麦成株期抗白粉病表型数据进行了多位点全基因组关联分析。
表1 637份河南省小麦核心种质明细表
SNP AX-109052670在四年田间环境中被5种关联分析方法共检测到12次，并且在他们的BLUP值环境中也能被重复检测到，将该位点命名为Qpm-3BL，该位点对总表型变异的解释比例为0.00％～12.98％。
对小麦成株期白粉病抗性位点Qpm-3BL所处的染色体区段进行了候选基因的预测。当上述637份河南省小麦核心种质的r2等于0.5时，这套实验材料的衰减距离约为750Kb。将在位于3BL上SNP AX-109052670两侧各750Kb范围内挑选候选基因，参考基因组1.0版本(http://202.194.139.32/)区间内共有68个注释基因。将这些基因在网站KOBAS3.0(http://kobas.cbi.pku.edu.cn/kobas3/？T＝1)上进行了KEGG分析，结果将这68个注释基因富集到了8个显著通路中(见表2)，其中植物病原菌互作通路中富集了2个被参考基因组功能注释为拥有植物抗病基因保守功能域(NBS-LRR)的基因，即TraesCS3B01G483700.1和TraesCS3B01G483600.1。为了进一步确定候选基因，首先从基因表达数据网站expVIP(http://www.wheat-expression.com/)下载了抗病小麦材料N9134第7天小麦叶片在接菌(E09)前及接菌后24h、48h和72h两个基因的表达数据，结果表明，接种小麦白粉病原菌(E09)48h后，这两个基因的表达量约为接种前的2倍。然后，又将TraesCS3B01G483700.1和TraesCS3B01G483600.1在NCBI(https:// blast.ncbi.nlm.nih.gov/Blast.cgi)网站上进行了同源比对，发现了一个与上面两个基因都有同源性且在之前被报道在大麦上也抗白粉病的基因RGA S-L8(GenBank:AJ507098.1)，用软件DNAMAN v9.0将该基因与TraesCS3B01G483600.1和TraesCS3B01G483700.1两基因蛋白序列进行比对，同源性分别为43.48％和94.17％(见图3)。综上所述，将TraesCS3B01G483700.1作为Qpm-3BL首选的候选基因，命名为PmBMYD，其DNA序列如SEQ ID NO:1所示，该基因表达的蛋白如SEQ.ID.NO:2所示。SEQ ID NO:1和SEQ.ID.NO:2展示序列为中国春参考基因组v.1.0版注释基因序列。
表2 QPm-3BL候选区间内68个注释基因的KEGG分析
二、KASP标记在亲本白蚂蚁蛋与濮麦9号的155个F2后代植株中的基因分型情况1、引物设计合成
在生信网站Triticeae Multi-omics Center(http://202.194.139.32/)中国春参考基因组(IWGSCv1.0)取小麦3BL上的位点SNP AX-109052670(730604593bp处)物理位置上下游各55bp(共111bp)提交给艾吉析科技(上海)有限公司(http:// sq23242284.china.herostart.com/)并由该公司设计合成KASP引物，序列如下：
Forward primer：
F1：5’-GAAGGTGACCAAGTTCATGCTTTGGAGGGGCTCCGACAAT-3’；
Forward primer:
F2：5’-GAAGGTCGGAGTCAACGGATTTTGGAGGGGCTCCGACAAC-3’；
Reverse primer：
R：5’-TCCACCACCAGTAGCTCCACACCACTCCAG-3’；
特异荧光序列FAM为5’-GAAGGTGACCAAGTTCATGCT-3’；
特异荧光序列HEX为5’-GAAGGTCGGAGTCAACGGATT-3’。
2、反应体系
DNA(50ng/ul),2×KASP Master mix,KASP Assay mix(100uM的Forward primer-F1，Forward primer-F2，Reverse primer-R三种引物和无菌水以12:12:30:46的体积比列混合物)。
反应体系：
| 384孔PCR板(uL/孔) | |
| 小麦基因组DNA | 2.5 |
| 2xKASP Master mix | 2.5 |
| KASP Assay mix | 0.07 |
| 总反应体系 | 5 |
3、反应程序
采用上述反应体系和反应程序对亲本白蚂蚁蛋与濮麦9号，以及二者的155个F2后代植株进行白粉病田间抗性鉴定和基因分型，结果见表3。
表3 KASP标记在亲本白蚂蚁蛋与濮麦9号的155个F2后代植株中的基因分型情况
表格中的抗病表型鉴定方法改自于石鹏皋(1987)的五级分类法，根据小麦上面四个小麦叶片发病程度进行评估。免疫：整蘖无病；高抗：旗叶和倒二叶发病程度1％以下，下部叶发病程度5％以下；中抗：旗叶和倒二叶发病程度1～5％，下部两片叶发病程度5～25％；中感：旗叶和倒二叶发病程度5～25％,下部叶片发病程度25～50％；高感：旗叶和倒二叶发病程度25％以上，下部叶片50％以上。分别用数字0、1、2、3和4代换免疫、高抗、中抗、中感和高感用于关联分析。
分型结果分布为含基因型TT的有40个株系，携有TC的69个，CC的46个，分离比符合1:2:1(χ2＝2.329,P-value＝0.3121)，说明设计的KASP标记是有效的。通过进一步统计各基因型中平均白粉病抗性情况，携有基因型TT，TC和CC的材料平均得分为1.53±1.05、1.59±1.05和2.06±1.31(P-value<0.05)，说明KASP标记在小麦抗白粉病分子辅助育种中是可用的。
以上所述之实施例，只是本发明的较佳实施例而已，并非限制本发明的实施范围，故凡依本发明专利范围所述的构造、特征及原理所做的等效变化或修饰，均应包括于本发明申请专利范围内。
SEQUENCE LISTING
<110> 河南省作物分子育种研究院
<120> 一种用于检测小麦成株期抗白粉病基因PmBMYD的KASP引物及其应用
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<160> 7
<170> PatentIn version 3.5
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atgagagctg tgtcccccgt gcttgttgat gccaaatcgc taacccgtgg tcaatctttc 60
ctgtcagttg cgcacgctgc tcggccccca acctattctg cttgactgac tgaacagttg 120
ttttgtcacc aggtaatgat tttgattgtg ctcagtttcc ctcaaaaaag ataaaaaatt 180
gattttgact gaatatgcac catgtcagat tagttcattc acagcttgca agtttcccaa 240
cacaactaaa atcgcatgtt gaacaaccaa ctaccttccc agaaaccaca taccatgtaa 300
ttagcactct ccttgtataa ttattagtac cctctccttc gaagaagcac acttctagca 360
tttttctgac ctgtataaca actgcaacta ttttgttcca taataagcat tagagttgca 420
tagttgatac aactatattc aagtcaagag tgtcaagtca tgcaaacgtg cgtgtagtac 480
tatgtattaa catgtcttaa atctttcctt ccttcatgct acggtttatc aggcccatga 540
gcaaaactct atatctcttt tcttatcacg gaccctgtta gtacttttgt ctgattatct 600
cagtgtcagt ctgtcagacg acaaaaagtg ttgattatac atatttatct agtactggta 660
gtacattgac accaggtatc ttctcccatg atacattaat aaaaaaaatt cttaaatatc 720
aacagagcta ctcgttccat ccatgcacga aaccagtgga gtaatgtcaa caaacctata 780
aattttcagt tcgaaaacta gtggaagtaa aacaaccatt ggagaaagtt tctctctgtt 840
catacaagct aagctaactc tcgacttaat tttcttggat gaaattggtt attgccccat 900
ttaacatatt gatctatatt tattttgttc aggacaaatg gcggaggcgg tgctcgttgc 960
tctcggaaag attgggaatg tcttagctga tgaagctacc aaggctttgc tggccaagct 1020
gtcagaaaaa gttagtaatc tgattgatct ggatgacaag attgagggaa tagcgaagca 1080
attaaataca atgaagaacg tcatacagca gataggcacg ccgtacctag ccgacaaagt 1140
cgtaaagggt tggattgggg aggtgaggaa gttggcctac catgttgagg atgtgatgga 1200
caaatactca tatcactctc ttcatgtgga aaaagggttt ctgaagaagt gcctcaaagg 1260
atcacattat gtccgggttt ttagtcaaat tgccgatgag gtagtcaaga tagagaagga 1320
gataaagcaa gttatcggac tcaaggagca atggctgcaa ccatcccagc ttgttcatga 1380
cccgtgcact gagatggaaa gacaacggtc ccaagatatc ttccctgaac ttgtgaaaga 1440
tgaagatctt attggaattg aagataacag gagaatgatg actgaatggt tgtactcgga 1500
tgagatggag actacggtga taacggtgtc gggtatgggt gggttgggaa aaacaaccct 1560
cgtcacaaat gtgtatgaac gtgaaaagat caacttccaa acaagtgcgt ggatggttgt 1620
gtctcagacc tacagtttgg atgctctgtt gaggaagtta ctcgagaagg ttaccgaaca 1680
accatcatca cctaacattg acaggatgga tgtgcatgac ttgaaggaag aaataaagcg 1740
aaagcttaaa gataggaaat gtttaattgt attggatgat gtctggaaca aggaagtgta 1800
ctctcaaatg cgagatgcat tccagaattc tcatgcaagt cgcatcatca tcacaacgcg 1860
gaacaatcat gttgctgctg ttgctcactt gacacgccgt atcgttctca agcctttggg 1920
gaatgctcac gcattcgaac tcttctgcag gagggtcttt tatatcaaga aggaccatga 1980
gtatgagtgt cccaatcatc tcatgaaaac tgctaggtct atagttgata gatgtcaggg 2040
tctgccacta gcaattttat caataggtgg tgttttgtct tcgaggccac aaacacaata 2100
ctcttgggag cagatataca atcaactctc aactgagctg tcgaagaatg atcatctccg 2160
ggcagtttta aatctgagct accatgacct atctggagac ctcagaaact gccttttgta 2220
ttgcagcctt ttcccggaag actacccgat gtcacgtgag agccttgtga ggctgtgggt 2280
tgcagaaggc tttgtgtgta gcaaaggaaa tagcaccccg gaggaggtgg ccgagggaaa 2340
cctgacggaa ctgatatacc gcaatatgct tgaagtcaag gagacagatg aactgggaag 2400
ggtgagcacc tgtacgatgc atgatattgt gcgagacctg gctctttgtg ttgcaagcga 2460
ggagcagttt gtatgtgcaa atgattatgc cacattgata catatgaata aggatgttcg 2520
tcgtctgtca tcatgtggat ggaaaggcaa tactgcactg aaaattaagc ttccccgtct 2580
tcgaactcta gtgtcagtag gagcaatttc atccatgcct gccatgccgt tctcagtttc 2640
gtcagaatcc agctacctga ctgtcctcga gctacaagac tctgaaatca ctgaagtgcc 2700
ggcatggata ggtacactct tcaatttaca ttacattggc ttacgccgca ccaaggtgag 2760
gtcactccca gactctgttg agaaactatc gaacctgcaa actctggaca tcaagcaaac 2820
taacatagag accctaccaa gagggattgc taagatcaag aatctacggc acctcttagc 2880
tgatagatat gctgatgaga agcagacgga gtttcgatac tttgtcggaa ttcaagcacc 2940
gaaagaactg cccaacattg aagggctgca gactcttgag accatccaag ccaacaaaga 3000
cttggctgag cagctggaga gaatggtgca attgcgaact ctgtggattg acaacataag 3060
ttctgctgaa tgcgcaacta tttttgctgc cctgtcaaat atgccgcttc tttccagtct 3120
gcttcttgct ggaagagatg agaacgaggc actttgtttc gagtccctcc agccaatgtc 3180
cacacatctc cacaagctga tcatcagagg gaaatgggcc aagggaacgc tggagtgccc 3240
gatattccgc agccacggag aaaatctcaa gtatctagct ctaagctggt gtcacctttg 3300
ggaagacgag gatccactgg ggatgcttgc accacacttg ccaaacctca catatctgcg 3360
gctcaacaac atgcgcagtg caaacatttt ggttctttct gcagattcct tccctcacct 3420
gaagagcctt acactgaagc acatgcataa tgtcaacgag ctaaagatca tcgatggcgc 3480
ccttccgagc atcgaaggtt tgtatgtcgt gtcattgtcg aagctggata aggtccctca 3540
aggcattgaa tcccttagtt ccctgaagaa gctctggctg ctgggcttgc acgggggctt 3600
caaagctcag tgggacaaga acggaatgca gcagaagatg gtgcatgttc aggagcttcg 3660
tgtctga 3667
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<212> DNA
<213> 人工序列（Artificial Seuqence）
<400> 4
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<210> 5
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<213> 人工序列（Artificial Sequence）
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<213> 人工序列（Artificial Sequence）
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<213> 人工序列（Artificial Sequence）
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gaaggtcgga gtcaacggat t 21
Claims (5)
1.一种用于检测小麦成株期抗白粉病基因PmBMYD的KASP引物，其特征在于，所述抗白粉病基因PmBMYD为核苷酸序列SEQ.ID.NO:1所示的DNA序列；
所述KASP引物由以下序列组成：
F1：5’-GAAGGTGACCAAGTTCATGCTTTGGAGGGGCTCCGACAAT-3’；
F2：5’-GAAGGTCGGAGTCAACGGATTTTGGAGGGGCTCCGACAAC-3’；
R：5’-TCCACCACCAGTAGCTCCACACCACTCCAG-3’；
特异荧光序列FAM：5’-GAAGGTGACCAAGTTCATGCT-3’ ；
特异荧光序列HEX：5’-GAAGGTCGGAGTCAACGGATT-3’。
2.根据权利要求1所述的一种用于检测小麦成株期抗白粉病基因PmBMYD的KASP标记，其特征在于，所述抗白粉病基因PmBMYD表达的蛋白为氨基酸序列SEQ.ID.NO:2所示的蛋白。
3.利用权利要求1所述的KASP引物对检测小麦成株期抗白粉病基因型的方法，其特征在于，包括如下步骤：
以待测小麦的基因组DNA为模板，用所述的KASP引物进行PCR扩增，然后根据检测到的荧光颜色判断样品基因型类型，红色表示基因型为CC，蓝色表示基因型为TT。
4.鉴定权利要求3所述小麦成株期抗白粉病基因型的试剂盒，其特征在于，所述试剂盒含有权利要求1 所述KASP引物。
5.权利要求1中所述的KASP引物在小麦抗白粉病分子辅助育种中的应用。
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